Related papers: Codon Usage Bias Measured Through Entropy Approach
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
We radically simplify coherently averaged dual-comb spectroscopy by introducing a real-time self-correction system: a radio frequency system-on-chip computes each incoming dual-comb interferogram's phase, frequency, and arrival time;…
Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily…
We present a genuine coherence measure based on a quasi-relative entropy as a difference between quasi-entropies of the dephased and the original states. The measure satisfies non-negativity and monotonicity under genuine incoherent…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
We study the measurement of transverse diffusion through beam echoes. We revisit earlier observations of echoes in RHIC and apply an updated theoretical model to these measurements. We consider three possible models for the diffusion…
The study of common heritability, or co-heritability, among multiple traits has been widely established in quantitative and molecular genetics. However, in bacteria, genome-based estimation of heritability has only been considered very…
We derive the effective channel for a logical qubit protected by an arbitrary quantum error-correcting code, and derive the map between channels induced by concatenation. For certain codes in the presence of single-bit Pauli errors, we…
Classification is a machine learning method used in many practical applications: text mining, handwritten character recognition, face recognition, pattern classification, scene labeling, computer vision, natural langage processing. A…
Divergence is not only an important mathematical concept in information theory, but also applied to machine learning problems such as low-dimensional embedding, manifold learning, clustering, classification, and anomaly detection. We…
In the present analysis we study the transition from coherent to incoherent dynamics in a nonlinear triplet of broad band combs of waves. Expanding the analysis of previous works, this paper investigates what happens when the band of…
The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to…
For many applications one wishes to decide whether a certain set of numbers originates from an equiprobability distribution or whether they are unequally distributed. Distributions of relative frequencies may deviate significantly from the…
Quantifying the similarity between symbolic sequences is a traditional problem in Information Theory which requires comparing the frequencies of symbols in different sequences. In numerous modern applications, ranging from DNA over music to…
In this paper will be presented new approach to entropy coding: family of generalizations of standard numeral systems which are optimal for encoding sequence of equiprobable symbols, into asymmetric numeral systems - optimal for freely…
Noise mechanisms in quantum systems can be broadly characterized as either coherent (i.e., unitary) or incoherent. For a given fixed average error rate, coherent noise mechanisms will generally lead to a larger worst-case error than…
Topological entropy has been one of the most difficult to implement of all the entropy-theoretic notions. This is primarily due to finite sample effects and high-dimensionality problems. In particular, topological entropy has been…
We propose and characterize experimentally a new source of optical frequency combs for performing multi-heterodyne spectrometry. This comb modality is based on a frequency shifting loop seeded with a CW monochromatic laser. The comb lines…
Gaussian mixture distributions are commonly employed to represent general probability distributions. Despite the importance of using Gaussian mixtures for uncertainty estimation, the entropy of a Gaussian mixture cannot be calculated…
Sampling from the output distribution of chaotic quantum evolutions, and of pseudo-random universal quantum circuits in particular, has been proposed as a prominent milestone for near-term quantum supremacy. The same paper notes that…